A day after The New York Times Company announced that it had dismissed Jill Abramson, The Times’s first female executive editor, it found itself mired in controversy, having to reassure employees and rebut reports that her removal was related to her complaints about receiving less pay than her male predecessors.

In announcing Ms. Abramson’s departure on Wednesday, the company said she had been fired only because of management issues, but through Thursday, a strong counternarrative had emerged in the news media — including the “Morning Joe” show on MSNBC and The New Yorker — that Ms. Abramson had been a victim of sexism by being held to a different standard than male editors.